# restrict dataset to relevant variables and change marker data to long format
dat_markers <- dat %>%
select(participant_id, timepoint, group, treatment, intervention, inter_treat,
gender, age, bmi_t0,
glucose, fructosamine, insulin,
tnfr2, il6, scrp, rage,
lbp, fabp2, zonulin,
contains("Acid")) %>%
pivot_longer(cols = all_of(c("glucose", "fructosamine", "insulin", "tnfr2", "il6", "scrp", "rage", "lbp", "fabp2", "zonulin",
"blood_methylbutyricAcid", "blood_aceticAcid", "blood_butyricAcid", "blood_hexanoicAcid",
"blood_isobutyricAcid", "blood_isovalericAcid", "blood_propionicAcid", "blood_valericAcid",
"stool_methylbutyricAcid", "stool_aceticAcid", "stool_butyricAcid", "stool_hexanoicAcid",
"stool_isobutyricAcid", "stool_isovalericAcid", "stool_propionicAcid", "stool_valericAcid")),
names_to = "marker")
# add marker group variable
dat_markers <- dat_markers %>%
mutate(marker_group = case_when(marker %in% metabolic_markers ~ "Metabolites",
marker %in% inflammation_markers ~ "Inflammation",
marker %in% leakyGut_markers ~ "Leaky gut",
marker %in% SCFA_bloodMarkers ~ "SCFA (blood)",
marker %in% SCFA_stoolMarkers ~ "SCFA (stool)",
marker %in% BCFA_bloodMarkers ~ "BCFA (blood)",
TRUE ~ "BCFA (stool)"),
marker = case_when(marker_group == "Metabolites" ~ names(metabolic_markers)[ match(marker, metabolic_markers)],
marker_group == "Inflammation" ~ names(inflammation_markers)[match(marker, inflammation_markers)],
marker_group == "Leaky gut" ~ names(leakyGut_markers)[ match(marker, leakyGut_markers)],
marker_group == "SCFA (blood)" ~ names(SCFA_bloodMarkers)[ match(marker, SCFA_bloodMarkers)],
marker_group == "SCFA (stool)" ~ names(SCFA_stoolMarkers)[ match(marker, SCFA_stoolMarkers)],
marker_group == "BCFA (blood)" ~ names(BCFA_bloodMarkers)[ match(marker, BCFA_bloodMarkers)],
TRUE ~ names(BCFA_stoolMarkers)[ match(marker, BCFA_stoolMarkers)]))